simlef.pyx - simulate loop extrusion in 1d with simulate()

looptools.py - analyse the structure of extruded loops:

• build trees of nested loops with get_parent_loops()
• find root loops with get_roots()
• identify the positions between the root loops with get_backbone()
• identify stacked LEFs with stack_lefs()

loopviz.py - visualize loops with plot_lefs()

loopviz_circular.py - visualize loops on the genome with plot_circular_genome_with_loops()

looplib_bacterial_gal folder:

• bacterial_no_bypassing.pyx - Simulate non-bypassing loop extrusion by LEF with simulate()

LEF_paths_gen.py - generate LEF paths on the genome several times and save into .h5 files